You should use ffmpeg, see
http://ffmpeg.gusari.org/viewtopic.php?f=11&t=1870
But at this time it seems that you only can set a title tag or to an audio resp. video stream a language tag
But if the name of the target file in the command line ends with .mkv instead of .webm you can set more metadata, like description tag. But then you have a matroska container.
An example call is:
ffmpeg -i tr3d.webm -c copy \
-metadata title="Moin Moin" \
-metadata license="CC-BY-NC-ND" \
-metadata description="Eine Fahrt im TR 09" \
-metadata copyright="Michael Dittmer" \
-metadata genre="Documentation" \
-metadata date_released="2014" \
-metadata url="http://www.pro-transrapid.org" \
-metadata artist="GFM-eV" \
-metadata publisher="Pro-Transrapid" \
-metadata:s:a:0 language="Spanish" \
tr3d_tagged.mkv